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- PDB-5b41: Crystal structure of VDR-LBD complexed with 2-methylidene-19-nor-... -

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Basic information

Entry
Database: PDB / ID: 5b41
TitleCrystal structure of VDR-LBD complexed with 2-methylidene-19-nor-1a,25-dihydroxyvitamin D3
Components
  • Mediator of RNA polymerase II transcription subunit 1
  • Vitamin D3 receptor
KeywordsTRANSCRIPTION / vitamin D3 / VDR / VDRE / RXR / co-factors
Function / homology
Function and homology information


negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / mammary gland branching involved in thelarche / retinal pigment epithelium development / SUMOylation of intracellular receptors ...negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / mammary gland branching involved in thelarche / retinal pigment epithelium development / SUMOylation of intracellular receptors / G0 to G1 transition / Nuclear Receptor transcription pathway / thyroid hormone receptor signaling pathway / response to bile acid / dense fibrillar component / core mediator complex / positive regulation of parathyroid hormone secretion / regulation of vitamin D receptor signaling pathway / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / cellular response to vitamin D / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / vitamin D binding / lithocholic acid binding / bile acid nuclear receptor activity / ventricular trabecula myocardium morphogenesis / thyroid hormone generation / mediator complex / nuclear retinoic acid receptor binding / positive regulation of keratinocyte differentiation / Generic Transcription Pathway / embryonic heart tube development / cellular response to thyroid hormone stimulus / negative regulation of ossification / positive regulation of vitamin D receptor signaling pathway / embryonic hindlimb morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of hepatocyte proliferation / vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / intestinal absorption / lens development in camera-type eye / nuclear thyroid hormone receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / embryonic hemopoiesis / megakaryocyte development / cellular response to steroid hormone stimulus / cellular response to hepatocyte growth factor stimulus / histone acetyltransferase binding / response to aldosterone / epithelial cell proliferation involved in mammary gland duct elongation / LBD domain binding / RSV-host interactions / fat cell differentiation / mammary gland branching involved in pregnancy / monocyte differentiation / regulation of calcium ion transport / decidualization / general transcription initiation factor binding / negative regulation of neuron differentiation / hematopoietic stem cell differentiation / negative regulation of keratinocyte proliferation / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / animal organ regeneration / erythrocyte development / heterochromatin / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / ubiquitin ligase complex / RNA polymerase II preinitiation complex assembly / keratinocyte differentiation / T-tubule / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / lactation / cellular response to epidermal growth factor stimulus / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of erythrocyte differentiation / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / liver development / skeletal system development / apoptotic signaling pathway / nuclear receptor binding / promoter-specific chromatin binding / nuclear estrogen receptor binding / positive regulation of transcription elongation by RNA polymerase II / animal organ morphogenesis / transcription coregulator activity / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / cell morphogenesis / euchromatin / brain development / PPARA activates gene expression / Cytoprotection by HMOX1
Similarity search - Function
: / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D receptor / VDR, DNA-binding domain / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. ...: / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / Vitamin D receptor / VDR, DNA-binding domain / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-YSV / Vitamin D3 receptor / Mediator of RNA polymerase II transcription subunit 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsAnami, Y. / Itoh, T. / Yamamoto, K.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics
Authors: Anami, Y. / Shimizu, N. / Ekimoto, T. / Egawa, D. / Itoh, T. / Ikeguchi, M. / Yamamoto, K.
History
DepositionMar 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin D3 receptor
C: Mediator of RNA polymerase II transcription subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5833
Polymers32,1662
Non-polymers4171
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-8 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.170, 41.750, 41.770
Angle α, β, γ (deg.)90.00, 96.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vitamin D3 receptor / VDR / 1 / 25-dihydroxyvitamin D3 receptor / Nuclear receptor subfamily 1 group I member 1


Mass: 30595.037 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 116-164, 212-423 / Mutation: 165-211 deletion
Source method: isolated from a genetically manipulated source
Details: deletion mutant, residues 165-211 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vdr, Nr1i1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13053
#2: Protein/peptide Mediator of RNA polymerase II transcription subunit 1


Mass: 1570.898 Da / Num. of mol.: 1 / Fragment: UNP residues 640-652 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15648
#3: Chemical ChemComp-YSV / (1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2- methylenecyclohexane-1,3-diol / 2-methylidene-19-nor-1alpha,25-dihydroxyvitamin D3


Mass: 416.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MOPS-Na, Na-formate, PEG 4000, Ethyleneglycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→35.02 Å / Num. obs: 20404 / % possible obs: 95.4 % / Redundancy: 3.1 % / Net I/σ(I): 11.2
Reflection shellResolution: 1.89→1.93 Å

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLC

2zlc


Resolution: 1.89→35.02 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.867 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23443 959 4.7 %RANDOM
Rwork0.18712 ---
obs0.18943 19445 94.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.724 Å2
Baniso -1Baniso -2Baniso -3
1--3.42 Å20 Å2-0.71 Å2
2--3.12 Å20 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.89→35.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 30 147 2182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192078
X-RAY DIFFRACTIONr_bond_other_d0.0060.022043
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.9962812
X-RAY DIFFRACTIONr_angle_other_deg0.92334720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.255247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59124.56592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6715382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9851511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212264
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02449
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7043.403997
X-RAY DIFFRACTIONr_mcbond_other3.7053.4996
X-RAY DIFFRACTIONr_mcangle_it5.3945.0621241
X-RAY DIFFRACTIONr_mcangle_other5.3915.0661242
X-RAY DIFFRACTIONr_scbond_it4.53.9321081
X-RAY DIFFRACTIONr_scbond_other4.4983.9311082
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9915.6661572
X-RAY DIFFRACTIONr_long_range_B_refined9.80528.0622523
X-RAY DIFFRACTIONr_long_range_B_other9.83627.7912479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.889→1.938 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 53 -
Rwork0.286 1412 -
obs--93.55 %

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